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Update SRMA test files so that functional tests pass

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This commit is contained in:
Kelly Vincent
2011-03-08 16:17:09 -05:00
parent b94de80659
commit a4f910c730
1 changed files with 4 additions and 4 deletions
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tools/sr_mapping/srma_wrapper.xml
+4 -4
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@@ -82,7 +82,7 @@
Prepare bam index file:
samtools index srma_in1.bam
Run SRMA:
java -jar "srma.jar" I=srma_in1.bam O=srma_out1.bam R=/afs/bx.psu.edu/depot/data/genome/hg18/srma_index/chr21.fa
java -jar srma.jar I=srma_in1.bam O=srma_out1.bam R=/afs/bx.psu.edu/depot/data/genome/hg18/srma_index/chr21.fa
To create the bam file first, start with a sam file (srma_in1.sam) generated with a run using the chr21 fasta file and which contains the header. Run before samtools index:
samtools view -bt /afs/bx.psu.edu/depot/data/genome/hg18/sam_index/chr21.fa -o srma_in1.u.bam srma_in1.sam
samtools sort srma_in1.u.bam srma_in1
@@ -97,13 +97,13 @@
<!-- Commands to run to prepare test files (uses custom genome):
Prepare custom dict/index files:
samtools faidx srma_in2.fa
java -cp "srma.jar" net.sf.picard.sam.CreateSequenceDictionary R=srma_in2.fa O=srma_in2.dict
java -cp srma.jar net.sf.picard.sam.CreateSequenceDictionary R=srma_in2.fa O=srma_in2.dict
Prepare bam index file:
samtools index srma_in3.bam
Run SRMA:
java -jar "srma.jar" I=srma_in3.bam O=srma_out2.bam R=srma_in2.fa OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=2 RANGES=null RANGE=null CORRECT_BASES=true USE_SEQUENCE_QUALITIES=true MAX_HEAP_SIZE=8192
To create the bam file first, the sam file needs to have been run with the same reference file (srma_in2.fa) and have the header present. Run these commands before samtools index:
samtools view -bt srma_in2.fa -o srma_in3.u.bam srma_in1.sam
To create the bam file first, the sam file needs to have been run with the same reference file (srma_in2.fa) and have the header present. For instance:
samtools view -bT srma_in2.fa -o srma_in3.u.bam srma_in3.sam
samtools sort srma_in3.u.bam srma_in3
-->
<param name="refGenomeSource_type" value="history" />